Table 1 Individual chromosomal islands of up- or down-regulation.
From: A genome-wide map of aberrantly expressed chromosomal islands in colorectal cancer
expression change | start region | end region | start gene | end gene | potential tumor genes, hereditary CRC, known chromosomal imbalances |
|---|---|---|---|---|---|
loss | 1p36.33 | 1p36.32 | TNFRSF18 | ARHGEF16 | amplification of 1p36.33-p32 in CRC [25] // deletion of 13p36.3 in 25% of neuroblastomas and 87% of cell lines [45] // loss of expression and genomic deletion on 1p [17] |
loss | 1p36.13 | 1p36.11 | PADI1 | DKFZP434L0117 | E2F2 // ID3 // loss of 1p36.1 in CRC [22, 25] // loss of expression and genomic deletion on 1p [17] |
loss | 1p35.1 | 1p34.3 | HDAC1 | PSMB2 | LCK at 1p35.1 // hereditary CRC at 1p35 (OMIM 114500) // loss of expression and genomic deletion on 1p [17] |
gain | 1q32.1 | 1q41 | PIGR | DKFZp547M236 | 1q32 amplification involving MDM4 and CNTN2 in malignant gliomas [46] |
gain | 2p25.3 | 2p24.2 | Hs.8379.0 | VSNL1 | hereditary CRC at 2p25 (OMIM 114500) |
loss | 2p11.2 | 2q12.1 | MAT2A | MGC11332 | 83% loss of 2p11 in mantle cell lymphoma [47] // loss in mantle cell lymphoma [48] |
gain | 2q31.3 | 2q32.2 | SSFA2 | NAB1 | hereditary HNPCC3 at 22q31-q33 (OMIM 600258) // familial breast cancer at 2q (OMIM 114480) |
gain | 2q33.2 | 2q35 | Hs.163603 | AAMP | familial breast cancer at 2q (OMIM 114480) |
loss | 2q37.3 | 2q37.3 | SCLY | FARP2 | familial breast cancer at 2q (OMIM 114480) |
gain | 3p25.3 | 3p25.1 | KIAA0121 | CAPN7 | amplification of 3p25.2 in CRC [25] // RAF1 at 3p25.2 // FBLN1 at 3p25.2 |
gain | 3p25.1 | 3p24.2 | RAFTLIN | THRB | Â |
gain | 3p24.2 | 3p23 | FLJ20604 | CLASP2 | Â |
loss | 3p21.31 | 3p21.31 | CELSR3 | NPR2L | hereditary HNPCC2 at 3p21.3 (OMIM 609310) // RASFF1 |
gain | 3p11.1 | 3q13.11 | MGC26717 | ALCAM | frequent 3q11.2-q13.1 amplifications in cervix carcinomas [49] |
loss | 3q13.13 | 3q21.2 | Hs.23762.0 | ITGB5 | Â |
loss | 4p15.32 | 4p14 | LAP3 | Hs.118993 | deletions of 4p14 in CRC [24] // SLIT2 at 4p15 is inactivated by hypermethylation in gliomas [33] // SLIT2 suppresses tumor growth [32] // loss of expression and genomic deletion on 1p [17] |
loss | 4q13.2 | 4q13.3 | YT521 | CXCL6 | global loss of expression and genomic deletion on 4 [17] |
loss | 4q21.21 | 4q22.3 | PRKG2 | LIM | transition of follicular B cell lymphoma to diffuse large cell lymphoma accompanied by 4q21-q23 deletions // global loss of expression and genomic deletion on 4 [17] |
loss | 4q34.1 | 4q35.2 | HPGD | Hs.130535 | deletion of 4q34-q35 in colorectal cancer cell lines [25] // CASP3 at 4q34.3 // global loss of expression and genomic deletion on 4 [17] |
loss | 5q15 | 5q23.2 | Hs.444378 | Hs.97104 | hereditary colorectal adenoma and carcinoma 1 (CRAC1) (OMIM 601228) at 15q15.3-q221 // APC at 5q21 // loss of expression and genomic deletion on 5q [17] |
gain | 5q31.1 | 5q31.3 | HTGN29 | Hs.443121 | loss of expression and genomic deletion on 5q [17] |
loss | 5q31.3 | 5q33.1 | NDFIP1 | FLJ10290 | amplification of 5q32-q34 in prostate cancer [50] // PDGFRB at 5q32 // loss of expression and genomic deletion on 5q [17] |
gain | 5q33.2 | 5q35.1 | MRPL22 | FBXW1B | amplification of 5q32-q34 in prostate cancer [50] // loss of expression and genomic deletion on 5q [17] |
gain | 6p25.3 | 6p24.2 | DUSP22 | NEDD9 | amplification of 6p25 in 24% of mantle cell lymphomas [47] // amplification of 6p25 in 75% of prostate cancers [51] |
loss | 6p22.3 | 6p22.2 | CAP2 | SLC17A4 | most frequent amplification of 6p22.3 in bladder cancer arrayCGH study [52] |
loss | 6p21.32 | 6p21.32 | PBX2 | RAB2L | Â |
gain | 6p21.31 | 6p21.2 | HMGA1 | RNF8 | CDKN1A at 6p21.2 // PIM1 at 6p21.2 |
gain | 6q23.3 | 6q24.2 | DUFD1 | Hs.12565 | amplification of 6q23-q24 assosicated with short survival [22] |
gain | 7p22.3 | 7p21.3 | FLJ23471 | ICA1 | hereditary HNPCC4 at 7p22 (gene PMS2) // gain of expression and genomic amplification of 7 [17] |
gain | 7p21.2 | 7p15.3 | ETV1 | OSBPL3 | amplification of 7p21 in mantle cell lymphomas [47] // amplification of 7p21 in osteosarcoma [53] // gain of expression and genomic amplification of 7 [17] |
gain | 7p14.3 | 7p13 | LSM5 | NPC1L1 | gain of expression and genomic amplification of 7 [17] |
loss | 7q11.23 | 7q21.3 | SRCRB4D | CAS1 | amplification of 7q11.1-q12 in metastatic CRC [24] // gain of expression and genomic amplification of 7 [17] |
gain | 7q31.31 | 7q33 | FAM3C | MGC5242 | prostate cancer aggressiveness linked to 7q32-q33 [54] // gain of expression and genomic amplification of 7 [17] |
gain | 8q11.23 | 8q21.11 | ATP6V1H | ANKTM1 | amplifications of 8q11-q24 in metastasing CRC [29] // LYN at 8q12.1 // MOS at 8q12.1 // familial breast cancer at 8q11 (OMIM 114480) // amplifications at 8q in CRC [18, 21, 23, 25] // gain of expression and genomic amplification of 8q [17] |
gain | 8q22.3 | 8q24.22 | TIEG | SLA | amplifications of 8q11-q24 in metastasing CRC [29] // MYC at 8q24.21 // PVT1 at 8q24.21 // amplification of 8q23-q24 in prostate cancer [55]// gain of expression and genomic amplification of 8q [17] |
loss | 9p21.3 | 9p21.1 | IFNA4 | SMU-1 | loss of 9p21 in CRC [25] // TUBE1 at 9p21 // CDKN2A alias p16INK4A at ??? // frequent deletion of 9p21 in prostate cancer [56] // deletion of 9p21.3 in bladder cancer [57] |
loss | 9p13.3 | 9p13.3 | BAG1 | OPRS1 | frequent LOH at 9p13-p21 in melanoma [58] |
loss | 9q21.11 | 9q21.32 | Hs.173519.0 | Hs.522256 | loss of 9q21-q22 in mantle cell lymphoma [59] |
loss | 9q34.11 | 9q34.11 | FLJ14596 | GPR107 | ABL1 protooncogene at 9q34.12 |
loss | 10p15.3 | 10p12.2 | Hs.255096 | Hs.57079.0 | frequent LOH of 10p15 in gastric cancer [60] // telomerase repressor at 10q15.1 [61] // deletion of 10p14 in mantle cell lymphoma [47, 59] // OPTN at 10p14 [62] |
loss | 10q11.21 | 10q11.23 | Hs.173866.0 | MOB | RET at 10q11.21 // LOH in prostate cancer at 10q11.21 [51] |
loss | 11p15.5 | 11p15.5 | RNH | MUC5AC | hereditary CRC at 11p15.5 / HRAS at 11p15.5 // 11p15.5 methylation-dependent expression silencing and imprinting in phaeochromocytomas [63] |
gain | 11p15.5 | 11p15.4 | CTSD | SSA1 | CTSD (Cathepsin D) at 11p15.5 // familial breast cancer at 11p15.5 (OMIM 114480) |
gain | 11p13 | 11p12 | Hs.120054.0 | TRAF6 | WT1 at 11p13 |
gain | 11p11.2 | 11q12.1 | ch-TOG | CTNND1 | Â |
loss | 11q13.2 | 11q13.4 | LOC338692 | SKD3 | BCL1 at 11q13.3 (anti-apoptotic, amplified in breast cancer) // CCND1 at 11q13.3 (amplified in breast cancer [64]) // FGF3 at 11q13 |
gain | 11q14.1 | 11q21 | Hs.26339.0 | MTMR2 | Â |
loss | 11q23.3 | 11q23.3 | AMICA | HYOU1 | frequent loss of 11q23.3-q25 in neuroblastoma [65] // loss of 11q23 in 33% of 73 tumor types [66] |
loss | 12p13.31 | 12p13.2 | TPI1 | CLEC1 | CDKN1B (alias p27Kip1) at 12p13.2 |
loss | 12p12.3 | 12q12 | CGI-26 | MADP-1 | familial breast cancer at 12p12.1 (OMIM 114480) |
gain | 12q14.2 | 12q22 | Hs.132260.0 | Hs.403150 | MDM2 at 12q15 // validated up-regulation of GPR49 at 12q21.1 |
gain | 12q22 | 12q23.3 | USP44 | KIAA1033 | Â |
loss | 12q23.3 | 12q24.11 | SART3 | Hs.18370.0 | loss of 12q24 in pancreas tumors [55] |
gain | 13q14.11 | 13q22.1 | LOC283508 | PIBF1 | RB1 at 13q14.2 // ARLT1 at 13q14 // gain of expression and genomic amplification of 13q [17] |
gain | 14q22.1 | 14q22.2 | PSMC6 | AND-1 | 14q22-q23 losses in 25% of tumor types [66] |
loss | 14q24.1 | 14q24.3 | Hs.369329 | Hs.169812 | hereditary CRC at 14q24.3 (OMIM 114500) // loss of 14q24-31 in CRC metastases [36] // FOS at 14q24.3 // hereditary HNPCC7 at 14q24.3 (gene MLH3) (OMIM) // poor prognosis when 14q24-q31 is lost in renal cell carcinoma [67] // loss of expression and genomic DNA of 14q [17] |
loss | 14q32.33 | 14q32.33 | ZFYVE21 | Hs.248015.0 | 14q32 is a tumor suppressive region in esophagal cancer [68] // loss of expression and genomic DNA of 14q [17] |
loss | 15q21.1 | 15q22.31 | FBN1 | CLPX | association between loss of 15q21.1-q22.2 and survival in hepatocellular carcinoma [69] // allelic imbalance at 15q21.1 in breast cancer metastases [70] // loss of expression and genomic DNA of 15q [17] |
loss | 15q26.1 | 15q26.3 | GABARAPL3 | FLJ25222 | loss of expression and genomic DNA of 15q [17] |
loss | 16p12.1 | 16p11.2 | GTF3C1 | PRSS8 | Â |
loss | 16q12.1 | 16q13 | TRF4-2 | FLJ13154 | Â |
gain | 16q22.1 | 16q22.2 | PSMB10 | KIAA0931 | CDH1 (E-Cadherin) at 16q22.1 |
loss | 17p13.3 | 17p13.2 | RPA1 | DHX33 | loss of 17p13.2 in CRC [25] // DHX33 at 17p13.2 |
loss | 17p13.1 | 17p11.2 | GAS7 | COPS3 | Near TP53 at 17p13.1 .// hereditary CRC at 17p11.2 (OMIM 114500) // hereditary CRC at 17p13.1 (OMIM 114500) // // familial breast cancer at 17p13 (OMIM 114480) // loss of 17p12 in CRC [25] // ELAC2 at 17p11.2 |
gain | 17q21.33 | 17q23.2 | TOB1 | PPM1D | NME1 (NME23) at 17q21.33 // familial breast cancer at 17q22-q23 (OMIM 114480) // |
loss | 18p11.21 | 18q12.1 | MGC24180 | DSC3 | loss of expression and genomic DNA of 18 [17] |
loss | 18q21.1 | 18q23 | CGBP | MBP | DCC at 18q21.3 (OMIM 120470) // loss of 18q21.1 in CRC cell lines [25] // SMAD2 // SMAD4 mutations in CRC [71] // loss of expression and genomic DNA of 18 [17] |
loss | 19p13.3 | 19p13.3 | DF | APCL | Â |
gain | 19p13.2 | 19p13.12 | FLJ20244 | NOTCH3 | Â |
gain | 19p13.11 | 19q13.12 | LOC114977 | TYROBP | NIFIE14 at 19q13.12 |
loss | 19q13.2 | 19q13.32 | MGC20255 | TOMM40 | AKT2 (breast carcinoma at 19q13.2 // TGFB1 at 19q13.2 // proapototic Bax at 19q13.33 |
gain | 20p11.21 | 20q11.21 | C1QR1 | BCL2L1 | Â |
gain | 20q11.22 | 20q11.23 | RNPC2 | C20orf102 | SRC at 20q11.23 (overexpressed in breast carcinoma) // gain of expression and genomic DNA of 20q [17] |
gain | 20q13.12 | 20q13.33 | SLC12A5 | ARFRP1 | gain of expression and genomic DNA of 20q [17] |
gain | 21q22.12 | 21q22.3 | C21orf18 | TMPRSS2 | ETS2 at 21q22.2 |
loss | 21q22.3 | 21q22.3 | PFKL | COL6A1 | COL18A1 (Endostatin) at 21q22.3 |
loss | 22q11.21 | 22q12.1 | SDF2L1 | TPST2 | familial breast cancer at 22q12.1 (OMIM 114480) |
loss | 22q13.31 | 22q13.33 | Hs.296370.0 | RABL2B | hereditary CRC at 22q13 (OMIM 114500) |
gain | Xp22.13 | Xp22.11 | SCML1 | ARX | Â |
gain | Xp11.22 | Xp11.1 | Hs.3383.1 | Hs.224455 | Â |
gain | Xq24 | Xq26.3 | FLJ32122 | CXX1 | Â |